void medResliceViewer::generateOutput(vtkImageReslice* reslicer, QString destType)
{
typedef itk::Image<DATA_TYPE, 3> ImageType;
typedef itk::VTKImageToImageFilter<ImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(reslicer->GetOutput());
filter->Update();
filter->GetOutput()->Update();
outputData = medAbstractDataFactory::instance()->createSmartPointer(destType);
outputData->setData(filter->GetOutput());
// Apply resampling in pix
if (reformaTlbx->findChild<QComboBox*>("bySpacingOrDimension")->currentText() == "Dimension")
{
applyResamplingPix();
}
typename ImageType::Pointer outputImage = static_cast<itk::Image<DATA_TYPE, 3>*>(outputData->data());
compensateForRadiologicalView<DATA_TYPE>(outputImage);
correctOutputTransform<DATA_TYPE>(outputImage, reslicer->GetResliceAxes());
// Final output image
outputData->setData(outputImage);
medUtilities::setDerivedMetaData(outputData, inputData, "reformatted");
medUtilitiesITK::updateMetadata<ImageType>(outputData);
}
void mitk::OtsuTool3D::CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, std::vector<int> regionIDs)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef itk::Image<mitk::Tool::DefaultSegmentationDataType, VImageDimension> OutputImageType;
typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
// InputImageType::Pointer itkImage;
typename OutputImageType::Pointer itkBinaryTempImage1;
typename OutputImageType::Pointer itkBinaryTempImage2;
typename OutputImageType::Pointer itkBinaryResultImage;
// mitk::Image::Pointer multiLabelSegmentation = dynamic_cast<mitk::Image*>(m_MultiLabelResultNode->GetData());
// mitk::CastToItkImage(multiLabelSegmentation, itkImage);
filter->SetInput(itkImage);
filter->SetLowerThreshold(regionIDs[0]);
filter->SetUpperThreshold(regionIDs[0]);
filter->SetInsideValue(1);
filter->SetOutsideValue(0);
filter->Update();
itkBinaryTempImage2 = filter->GetOutput();
typename itk::OrImageFilter<OutputImageType, OutputImageType>::Pointer orFilter =
itk::OrImageFilter<OutputImageType, OutputImageType>::New();
// if more than one region id is used compute the union of all given binary regions
for (std::vector<int>::iterator it = regionIDs.begin(); it != regionIDs.end(); ++it)
{
filter->SetLowerThreshold(*it);
filter->SetUpperThreshold(*it);
filter->SetInsideValue(1);
filter->SetOutsideValue(0);
filter->Update();
itkBinaryTempImage1 = filter->GetOutput();
orFilter->SetInput1(itkBinaryTempImage1);
orFilter->SetInput2(itkBinaryTempImage2);
orFilter->UpdateLargestPossibleRegion();
itkBinaryResultImage = orFilter->GetOutput();
itkBinaryTempImage2 = itkBinaryResultImage;
}
//----------------------------------------------------------------------------------------------------
mitk::Image::Pointer binarySegmentation;
mitk::CastToMitkImage(itkBinaryResultImage, binarySegmentation);
m_BinaryPreviewNode->SetData(binarySegmentation);
m_BinaryPreviewNode->SetVisibility(true);
m_BinaryPreviewNode->SetProperty("outline binary", mitk::BoolProperty::New(false));
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void DoubleThresholdImageFilterITK::doubleThresholdImageFilterITK() {
insideValue_.setVolume(inport1_.getData());
outsideValue_.setVolume(inport1_.getData());
threshold1_.setVolume(inport1_.getData());
threshold2_.setVolume(inport1_.getData());
threshold3_.setVolume(inport1_.getData());
threshold4_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::DoubleThresholdImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetInsideValue(insideValue_.getValue<T>());
filter->SetOutsideValue(outsideValue_.getValue<T>());
filter->SetThreshold1(threshold1_.getValue<T>());
filter->SetThreshold2(threshold2_.getValue<T>());
filter->SetThreshold3(threshold3_.getValue<T>());
filter->SetThreshold4(threshold4_.getValue<T>());
filter->SetFullyConnected(fullyConnected_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void ComputeMaskedIsophotesInRegion(const TVectorImageType* const image, const Mask* const mask,
const itk::ImageRegion<2>& region, TIsophoteImageType* const outputIsophotes)
{
//Helpers::WriteImageConditional<FloatScalarImageType>(image, "Debug/ComputeMaskedIsophotes.luminance.mha",
// this->DebugImages);
typename TIsophoteImageType::Pointer gradient = TIsophoteImageType::New();
ITKHelpers::InitializeImage(gradient.GetPointer(), image->GetLargestPossibleRegion());
Derivatives::MaskedGradientInRegion(image, mask, region, gradient.GetPointer());
//Helpers::DebugWriteImageConditional<FloatVector2ImageType>(gradient,
// "Debug/ComputeMaskedIsophotes.gradient.mha", this->DebugImages);
//Helpers::Write2DVectorImage(gradient, "Debug/ComputeMaskedIsophotes.gradient.mha");
// Rotate the gradient 90 degrees to obtain isophotes from gradient
typedef itk::UnaryFunctorImageFilter<TIsophoteImageType, TIsophoteImageType,
RotateVectors<typename TIsophoteImageType::PixelType,
typename TIsophoteImageType::PixelType> > FilterType;
typename FilterType::Pointer rotateFilter = FilterType::New();
rotateFilter->SetInput(gradient);
rotateFilter->Update();
//Helpers::DebugWriteImageConditional<FloatVector2ImageType>(rotateFilter->GetOutput(),
// "Debug/ComputeMaskedIsophotes.Isophotes.mha", this->DebugImages);
//Helpers::Write2DVectorImage(rotateFilter->GetOutput(), "Debug/ComputeMaskedIsophotes.Isophotes.mha");
ITKHelpers::CopyRegion(rotateFilter->GetOutput(), outputIsophotes, region, region);
}
void mitk::CLUtil::itkGaussianFilter(TImageType * image, mitk::Image::Pointer & smoothed ,double sigma)
{
typedef itk::DiscreteGaussianImageFilter<TImageType,TImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(image);
filter->SetVariance(sigma);
filter->Update();
mitk::CastToMitkImage(filter->GetOutput(),smoothed);
}
void mitk::CLUtil::itkFillHoleGrayscale(TImageType * image, mitk::Image::Pointer & outimage)
{
typedef itk::GrayscaleFillholeImageFilter<TImageType,TImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(image);
filter->Update();
mitk::CastToMitkImage(filter->GetOutput(),outimage);
}
void DiscreteGaussianImageFilterITK::discreteGaussianImageFilterITK() {
maximumError_.setVolume(inport1_.getData());
maximumError_.setMinValue<T>(1.0f);
variance_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<float, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::DiscreteGaussianImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetInternalNumberOfStreamDivisions(internalNumberOfStreamDivisions_.get());
filter->SetMaximumError(maximumError_.getValue<T>());
filter->SetVariance(variance_.getValue<T>());
filter->SetUseImageSpacing(useImageSpacing_.get());
filter->SetFilterDimensionality(filterDimensionality_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<float>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void IntensityWindowingImageFilterITK::intensityWindowingImageFilterITK() {
outputMinimum_.setVolume(inport1_.getData());
outputMaximum_.setVolume(inport1_.getData());
windowMinimum_.setVolume(inport1_.getData());
windowMaximum_.setVolume(inport1_.getData());
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::IntensityWindowingImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetOutputMinimum(outputMinimum_.getValue<T>());
filter->SetOutputMaximum(outputMaximum_.getValue<T>());
filter->SetWindowMinimum(windowMinimum_.getValue<T>());
filter->SetWindowMaximum(windowMaximum_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void BayesianClassifierImageFilterITK::bayesianClassifierImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType;
typedef itk::Image<uint8_t, 3> OutputImageType;
typedef itk::VectorImage<float, 3> VectorImageType;
typename InputImageType::Pointer p1 = voreenToITK<T>(inport1_.getData());
typedef itk::BayesianClassifierInitializationImageFilter<InputImageType> InitFilterType;
typename InitFilterType::Pointer initializer = InitFilterType::New();
initializer->SetInput(p1);
initializer->SetNumberOfClasses(numberOfClasses_.get());
try
{
initializer->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
//Filter define
typedef itk::BayesianClassifierImageFilter<VectorImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(0, initializer->GetOutput());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<uint8_t>(filter->GetOutput());
if (outputVolume1) {
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
}
else
outport1_.setData(0);
}
void OtsuThresholdImageFilterITK::otsuThresholdImageFilterITK() {
outsideValue_.setVolume(inport1_.getData());
outsideValue_.setMinValue<T>(0.0001f);
insideValue_.setVolume(inport1_.getData());
insideValue_.setMinValue<T>(0.0001f);
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::OtsuThresholdImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetNumberOfHistogramBins(numberOfHistogramBins_.get());
filter->SetOutsideValue(outsideValue_.getValue<T>());
filter->SetInsideValue(insideValue_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void AddOffset(itk::Image<TPixel, VImageDimension>* image, int offset, mitk::Image::Pointer outputImage)
{
typedef itk::Image<TPixel, VImageDimension> ImageType;
typedef itk::ShiftScaleInPlaceImageFilter<ImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetShift(offset);
filter->SetInput(image);
filter->Update();
mitk::CastToMitkImage(filter->GetOutput(), outputImage);
}
void NarrowBandThresholdSegmentationLevelSetImageFilterITK::narrowBandThresholdSegmentationLevelSetImageFilterITK() {
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::NarrowBandThresholdSegmentationLevelSetImageFilter<InputImageType1, InputImageType2> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetFeatureImage(p2);
filter->SetPropagationScaling(propagationScaling_.get());
filter->SetCurvatureScaling(curvatureScaling_.get());
filter->SetAdvectionScaling(advectionScaling_.get());
filter->SetMaximumRMSError(maximumRMSError_.get());
filter->SetNumberOfIterations(numberOfIterations_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void GradientRecursiveGaussianImageFilterITK::gradientRecursiveGaussianImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<itk::CovariantVector<double,3>, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::GradientRecursiveGaussianImageFilter<InputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetNormalizeAcrossScale(normalizeAcrossScale_.get());
filter->SetUseImageDirection(useImageDirection_.get());
filter->SetSigma(sigma_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKVec3ToVoreenVec3Copy<double>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void GradientAnisotropicDiffusionImageFilterITK::gradientAnisotropicDiffusionImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::GradientAnisotropicDiffusionImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetNumberOfIterations(numberOfIterations_.get());
filter->SetTimeStep(timeStep_.get());
filter->SetConductanceParameter(conductanceParameter_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void ScalarConnectedComponentImageFilterITK::scalarConnectedComponentImageFilterITK() {
distanceThreshold_.setVolume(inport1_.getData());
distanceThreshold_.setMinValue<T>(0.001f);
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::ScalarConnectedComponentImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetDistanceThreshold(distanceThreshold_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void RelabelComponentImageFilterITK::relabelComponentImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::RelabelComponentImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetMinimumObjectSize(minimumObjectSize_.get());
observe(filter.GetPointer());
try
{
filter->Update();
numberOfObjects_.set(filter->GetNumberOfObjects());
originalNumberOfObjects_.set(filter->GetOriginalNumberOfObjects());
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void LabelOverlayImageFilterITK::labelOverlayImageFilterITK() {
backgroundValue_.setVolume(inport1_.getData());
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typedef itk::Image<itk::CovariantVector<uint8_t,3>, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::LabelOverlayImageFilter<InputImageType1, InputImageType2, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetLabelImage(p2);
filter->SetOpacity(opacity_.get());
filter->SetBackgroundValue(backgroundValue_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKVec3ToVoreenVec3Copy<uint8_t>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void mitk::CLUtil::itkDilateGrayscale(TImageType * image, mitk::Image::Pointer & outimage , unsigned int radius, mitk::CLUtil::MorphologicalDimensions d)
{
typedef itk::BinaryBallStructuringElement<typename TImageType::PixelType, 3> StructureElementType;
typedef itk::GrayscaleDilateImageFilter<TImageType,TImageType,StructureElementType> FilterType;
StructureElementType ball;
itkFitStructuringElement(ball,d, radius);
typename FilterType::Pointer filter = FilterType::New();
filter->SetKernel(ball);
filter->SetInput(image);
filter->Update();
mitk::CastToMitkImage(filter->GetOutput(),outimage);
}
void VotingBinaryIterativeHoleFillingImageFilterITK::votingBinaryIterativeHoleFillingImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::VotingBinaryIterativeHoleFillingImageFilter<InputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetMaximumNumberOfIterations(maximumNumberOfIterations_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void GrayscaleGrindPeakImageFilterITK::grayscaleGrindPeakImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::GrayscaleGrindPeakImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetFullyConnected(fullyConnected_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void MinMaxCurvatureFlowImageFilterITK::minMaxCurvatureFlowImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<float, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::MinMaxCurvatureFlowImageFilter<InputImageType1, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetStencilRadius(stencilRadius_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<float>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void WatershedImageFilterITK::watershedImageFilterITK() {
if (!enableProcessing_.get()) {
outport1_.setData(inport1_.getData(), false);
return;
}
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<VolumeRAM_UInt64, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
//Filter define
typedef itk::WatershedImageFilter<InputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetLevel(level_.get());
filter->SetThreshold(threshold_.get());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<itk::IdentifierType>(filter->GetOutput());
if (outputVolume1) {
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
}
else
outport1_.setData(0);
}
void MaskImageFilterITK::maskImageFilterITK() {
outsideValue_.setVolume(inport1_.getData());
typedef itk::Image<T, 3> InputImageType1;
typedef itk::Image<S, 3> InputImageType2;
typedef itk::Image<T, 3> OutputImageType1;
typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());
typename InputImageType2::Pointer p2 = voreenToITK<S>(inport2_.getData());
//Filter define
typedef itk::MaskImageFilter<InputImageType1, InputImageType2, OutputImageType1> FilterType;
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p1);
filter->SetMaskImage(p2);
filter->SetOutsideValue(outsideValue_.getValue<T>());
observe(filter.GetPointer());
try
{
filter->Update();
}
catch (itk::ExceptionObject &e)
{
LERROR(e);
}
Volume* outputVolume1 = 0;
outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());
if (outputVolume1) {
transferRWM(inport1_.getData(), outputVolume1);
transferTransformation(inport1_.getData(), outputVolume1);
outport1_.setData(outputVolume1);
} else
outport1_.setData(0);
}
void mitk::ShImage::Construct() const
{
typedef itk::Image<itk::Vector<float, ( nShOrder * nShOrder + nShOrder + 2)/2 + nShOrder >,3> ImageType;
typedef itk::ShToRgbImageFilter<ImageType, nShOrder> FilterType;
typename FilterType::Pointer filter = FilterType::New();
typename ImageType::Pointer itkvol = ImageType::New();
mitk::CastToItkImage(this, itkvol);
filter->SetInput(itkvol);
filter->Update();
itk::Image<itk::RGBAPixel<unsigned char>,3>::Pointer tmp = filter->GetOutput();
m_RgbImage = mitk::Image::New();
m_RgbImage->InitializeByItk( tmp.GetPointer() );
m_RgbImage->SetVolume( tmp->GetBufferPointer() );
}
typename ImageType::Pointer convolveImageHelper(
typename ImageType::Pointer image,
typename ImageType::Pointer kernel )
{
enum { Dimension = ImageType::ImageDimension };
if( image.IsNotNull() & kernel.IsNotNull() )
{
typedef itk::ConvolutionImageFilter<ImageType> FilterType;
typename FilterType::Pointer convolutionFilter = FilterType::New();
convolutionFilter->SetInput( image );
convolutionFilter->SetKernelImage( kernel );
convolutionFilter->Update();
return convolutionFilter->GetOutput();
}
return NULL;
}
int itkFiltersComponentSizeThresholdProcess::updateProcess(medAbstractData* inputData)
{
dtkSmartPointer<medAbstractData> adjustedInputData = inputData;
if (std::is_floating_point<typename InputImageType::PixelType>::value)
{
adjustedInputData = castToOutputType<InputImageType>(inputData);;
}
typename InputImageType::Pointer inputImage = static_cast<InputImageType*>(inputData->data());
typedef itk::ConnectedComponentImageFilter <InputImageType, OutputImageType> ConnectedComponentFilterType;
typename ConnectedComponentFilterType::Pointer connectedComponentFilter = ConnectedComponentFilterType::New();
connectedComponentFilter->SetInput(inputImage);
connectedComponentFilter->Update();
// RELABEL COMPONENTS according to their sizes (0:largest(background))
typedef itk::RelabelComponentImageFilter<OutputImageType, OutputImageType> FilterType;
typename FilterType::Pointer relabelFilter = FilterType::New();
relabelFilter->SetInput(connectedComponentFilter->GetOutput());
relabelFilter->SetMinimumObjectSize(d->minimumSize);
relabelFilter->Update();
// BINARY FILTER
typedef itk::BinaryThresholdImageFilter <OutputImageType, OutputImageType> BinaryThresholdImageFilterType;
typename BinaryThresholdImageFilterType::Pointer thresholdFilter
= BinaryThresholdImageFilterType::New();
thresholdFilter->SetInput(relabelFilter->GetOutput());
thresholdFilter->SetUpperThreshold(0);
thresholdFilter->SetInsideValue(0);
thresholdFilter->SetOutsideValue(1);
thresholdFilter->Update();
itk::CStyleCommand::Pointer callback = itk::CStyleCommand::New();
callback->SetClientData ( ( void * ) this );
callback->SetCallback ( itkFiltersProcessBase::eventCallback );
connectedComponentFilter->AddObserver ( itk::ProgressEvent(), callback );
setOutputData(medAbstractDataFactory::instance()->createSmartPointer(medUtilitiesITK::itkDataImageId<OutputImageType>()));
getOutputData()->setData ( thresholdFilter->GetOutput() );
QString newSeriesDescription = "connectedComponent " + QString::number(d->minimumSize);
medUtilities::setDerivedMetaData(getOutputData(), inputData, newSeriesDescription);
return DTK_SUCCEED;
}
void mitk::CLUtil::itkClosingBinary(TImageType * sourceImage, mitk::Image::Pointer& resultImage, int factor, MorphologicalDimensions d)
{
typedef TImageType ImageType;
typedef itk::BinaryBallStructuringElement<typename TImageType::PixelType, 3> BallType;
typedef itk::BinaryMorphologicalClosingImageFilter<TImageType, TImageType, BallType> FilterType;
BallType strElem;
itkFitStructuringElement(strElem,d,factor);
typename FilterType::Pointer erodeFilter = FilterType::New();
erodeFilter->SetKernel(strElem);
erodeFilter->SetInput(sourceImage);
erodeFilter->SetForegroundValue(1);
erodeFilter->Update();
mitk::CastToMitkImage(erodeFilter->GetOutput(), resultImage);
}
Volume* ValuedRegionalMaximaImageFilter::applyFilter(const VolumeBase* inputVolume) {
typedef itk::Image<T, 3> InputImageType;
typedef itk::Image<T, 3> OutputImageType;
typename InputImageType::Pointer p = voreenToITK<T>(inputVolume);
typedef itk::ValuedRegionalMaximaImageFilter<InputImageType, OutputImageType> FilterType;
// Create the filter
typename FilterType::Pointer filter = FilterType::New();
filter->SetInput(p);
observe(filter.GetPointer());
// Run the filter
filter->Update();
return ITKToVoreenCopy<T>(filter->GetOutput());
}
medAbstractJob::medJobExitStatus medItkErodeImageProcess::_run()
{
typedef itk::Image<inputType, 3> ImageType;
typename ImageType::Pointer in = dynamic_cast<ImageType *>((itk::Object*)(this->input()->data()));
if(in.IsNotNull())
{
typedef itk::BinaryBallStructuringElement<inputType, 3> KernelType;
typedef itk::GrayscaleErodeImageFilter<ImageType, ImageType, KernelType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
m_filter = filter;
KernelType kernel;
kernel.SetRadius(this->kernelRadius()->value());
kernel.CreateStructuringElement();
filter->SetKernel(kernel);
filter->SetInput(in);
itk::CStyleCommand::Pointer callback = itk::CStyleCommand::New();
callback->SetClientData((void*)this);
callback->SetCallback(medItkErodeImageProcess::eventCallback);
filter->AddObserver(itk::ProgressEvent(), callback);
try
{
filter->Update();
}
catch(itk::ProcessAborted &e)
{
return medAbstractJob::MED_JOB_EXIT_CANCELLED;
}
medAbstractImageData *out= dynamic_cast<medAbstractImageData *>(medAbstractDataFactory::instance()->create(this->input()->identifier()));
out->setData(filter->GetOutput());
this->setOutput(out);
return medAbstractJob::MED_JOB_EXIT_SUCCESS;
}
return medAbstractJob::MED_JOB_EXIT_FAILURE;
}
typename TInputImage::Pointer SegmentationIntensityAndTextureImages<TInputImage>::getTextureImage()
{
typedef itk::ScalarToTextureRLImageFilter<ImageType,ImageType> FilterType;
typename FilterType::Pointer textureFilter = FilterType::New();
textureFilter->SetInput(inputImage);
textureFilter->SetTextureFeature(8);
typename FilterType::RegionSizeType size;
size.Fill(13);
textureFilter->SetRegionSize(size);
textureFilter->Update();
typename RescaleFilterType::Pointer normalizeFilter = RescaleFilterType::New();
normalizeFilter->SetOutputMaximum(255);
normalizeFilter->SetOutputMinimum(0);
normalizeFilter->SetInput(textureFilter->GetOutput());
normalizeFilter->Update();
return normalizeFilter->GetOutput();
}
